HTML has its own set of visual cues that you and millions of others easily interact with every single day. I would argue that the interaction model of HTML/JS apps may be as familiar or more familiar to users.
I don't disagree that HTML/JS apps can be difficult to develop, but I do not think they are going to "lose". (I don't think they are going to win either. It's not a win/lose situation.)
Since it seems that your background is in native applications, I just wanted to provide you with some references to frameworks that provide something a little more advanced than jQuery and interactive documents.
Obviously, each team needs to look at its project and goals and choose whether a native app, an HTML/JS app, or both is appropriate.